X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.cpp;h=85eed5207ff20d586bd999f670d59a4c8e840c67;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=cae2b92885632b697852babccd84d463b7a78564;hpb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;p=mothur.git

diff --git a/weighted.cpp b/weighted.cpp
index cae2b92..85eed52 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -13,15 +13,15 @@
 
 EstOutput Weighted::getValues(Tree* t, int p, string o) {
     try {
-		globaldata = GlobalData::getInstance();
-		
 		data.clear(); //clear out old values
 		int numGroups;
 		vector<double> D;
 		processors = p;
 		outputDir = o;
+        
+        TreeMap* tmap = t->getTreeMap();
 		
-		numGroups = globaldata->Groups.size();
+		numGroups = m->getNumGroups();
 		
 		if (m->control_pressed) { return data; }
 		
@@ -31,14 +31,14 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 			for (int l = 0; l < i; l++) {	
 				//initialize weighted scores
 				//WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
-				vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
+				vector<string> groups; groups.push_back((m->getGroups())[i]); groups.push_back((m->getGroups())[l]);
 				namesOfGroupCombos.push_back(groups);
 			}
 		}
 		
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			if(processors == 1){
-				data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+				data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
 			}else{
 				int numPairs = namesOfGroupCombos.size();
 				
@@ -52,12 +52,12 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 					lines.push_back(linePair(startPos, numPairsPerProcessor));
 				}
 
-				data = createProcesses(t, namesOfGroupCombos);
+				data = createProcesses(t, namesOfGroupCombos, tmap);
 				
 				lines.clear();
 			}
 		#else
-			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+			data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
 		#endif
 		
 		return data;
@@ -69,9 +69,9 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 }
 /**************************************************************************************************/
 
-EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, TreeMap* tmap) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		vector<int> processIDS;
 		
@@ -87,9 +87,9 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
 			}else if (pid == 0){
 	
 				EstOutput Myresults;
-				Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
+				Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, tmap);
 			
-				m->mothurOut("Merging results."); m->mothurOutEndLine();
+				//m->mothurOut("Merging results."); m->mothurOutEndLine();
 				
 				//pass numSeqs to parent
 				ofstream out;
@@ -110,7 +110,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
 			}
 		}
 	
-		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
+		results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, tmap);
 	
 		//force parent to wait until all the processes are done
 		for (int i=0;i<(processors-1);i++) { 
@@ -141,10 +141,10 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
 				m->gobble(in);
 			}
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 		
-		m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+		//m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 		
 		return results;
 #endif		
@@ -155,7 +155,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
 	}
 }
 /**************************************************************************************************/
-EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) { 
+EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, TreeMap* tmap) { 
  try {
 		EstOutput results;
 		vector<double> D;
@@ -267,9 +267,10 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
 /**************************************************************************************************/
 EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) { 
  try {
-		globaldata = GlobalData::getInstance();
 		
 		data.clear(); //clear out old values
+     
+        TreeMap* tmap = t->getTreeMap();
 		
 		if (m->control_pressed) { return data; }